In my log file (workspace_dir\.metadata\.log), I saw following exception:
org.eclipse.core.internal.dtree.ObjectNotFoundException: Tree element 'mypckg/myClass.class' not found.at org.eclipse.core.internal.dtree.AbstractDataTree.handleNotFound(AbstractDataTree.java:257)
at org.eclipse.core.internal.dtree.DeltaDataTree.getData(DeltaDataTree.java:585)
at org.eclipse.core.internal.dtree.DataDeltaNode.asBackwardDelta(DataDeltaNode.java:50)
at org.eclipse.core.internal.dtree.DataDeltaNode.asBackwardDelta(DataDeltaNode.java:47)
at org.eclipse.core.internal.dtree.DataDeltaNode.asBackwardDelta(DataDeltaNode.java:47)
at org.eclipse.core.internal.dtree.DataDeltaNode.asBackwardDelta(DataDeltaNode.java:47)
at org.eclipse.core.internal.dtree.DataDeltaNode.asBackwardDelta(DataDeltaNode.java:47)
After some research I tried to delete the workspace_dir\.metadata\.plugins\org.eclipse.core.resources\.snap file, which solved the problem. Don't ask me why. You can tell me why if you know :-)